[Open Babel] obgrep - aromaticity / kekule + molecule name bug
Hi all, With file.smi being C1=CC=CC=C1 single-double c1c1 aro c1c1N obgrep C1=CC=CC=C1 file.smi gives no output. But in my opinion, all 3 molecules should be matched. I'm pretty sure this problem was already discussed, but I found only this post http://forums.openbabel.org/Fw-Re-substructure-search-problem-td4655860.html These problems may be related? And the output of obgrep c1c1 file.smi is: c1c1single-double c1c1aro c1c1Naro It's fine, apart the 3rd compound name (there should be no compound name). In my tests, a no-name compound has the name of the preceding molecule (this preceding molecule being matched or not). Regards, Pascal -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obgrep - aromaticity / kekule + molecule name bug
If obabel does it, it always does it better: C:\Users\noelobabel -:C1=CC=CC=C1 single-double -:c1c1 aro -:c1c1N -s c1c1 -osmi c1c1single-double c1c1aro c1c1N 3 molecules converted I'm in favour of replacing all obgrep, etc. with symlinks to obabel. - Noel On 8 August 2013 08:38, Pascal Muller pascal.jm.mul...@gmail.com wrote: Hi all, With file.smi being C1=CC=CC=C1 single-double c1c1 aro c1c1N obgrep C1=CC=CC=C1 file.smi gives no output. But in my opinion, all 3 molecules should be matched. I'm pretty sure this problem was already discussed, but I found only this post http://forums.openbabel.org/Fw-Re-substructure-search-problem-td4655860.html These problems may be related? And the output of obgrep c1c1 file.smi is: c1c1single-double c1c1aro c1c1Naro It's fine, apart the 3rd compound name (there should be no compound name). In my tests, a no-name compound has the name of the preceding molecule (this preceding molecule being matched or not). Regards, Pascal -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obgrep - aromaticity / kekule + molecule name bug
I think it would be easy to add as a general option to all filters. Chris? In the meanwhile, wc -l will work I guess (needs Cygwin on windows). - Noel On 8 August 2013 09:38, Pascal Muller pascal.jm.mul...@gmail.com wrote: If obabel does it, it always does it better: (...) Ok... I need to think to the -s option instead of obgrep, then. I found the -v option (invert the matching), but is there an equivalent to the obgrep -c option (number of matches)? I'm in favour of replacing all obgrep, etc. with symlinks to obabel. Maybe a good idea. Many thanks, Pascal -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obgrep - aromaticity / kekule + molecule name bug
Or just look at stderr, where it prints 3 molecules converted. - Noel On 8 August 2013 09:43, Noel O'Boyle baoille...@gmail.com wrote: I think it would be easy to add as a general option to all filters. Chris? In the meanwhile, wc -l will work I guess (needs Cygwin on windows). - Noel On 8 August 2013 09:38, Pascal Muller pascal.jm.mul...@gmail.com wrote: If obabel does it, it always does it better: (...) Ok... I need to think to the -s option instead of obgrep, then. I found the -v option (invert the matching), but is there an equivalent to the obgrep -c option (number of matches)? I'm in favour of replacing all obgrep, etc. with symlinks to obabel. Maybe a good idea. Many thanks, Pascal -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obgrep - aromaticity / kekule + molecule name bug
With the obabel -s option you can specify the number of matches within a single molecule, e.g. find molecules with more than 2 benzene rings. Try obabel -L ops s for details. (Maybe obgrep's c option was originally going to do this?) Chris On 08/08/2013 09:43, Noel O'Boyle wrote: Or just look at stderr, where it prints 3 molecules converted. - Noel On 8 August 2013 09:43, Noel O'Boyle baoille...@gmail.com wrote: I think it would be easy to add as a general option to all filters. Chris? In the meanwhile, wc -l will work I guess (needs Cygwin on windows). - Noel On 8 August 2013 09:38, Pascal Muller pascal.jm.mul...@gmail.com wrote: If obabel does it, it always does it better: (...) Ok... I need to think to the -s option instead of obgrep, then. I found the -v option (invert the matching), but is there an equivalent to the obgrep -c option (number of matches)? I'm in favour of replacing all obgrep, etc. with symlinks to obabel. Maybe a good idea. Many thanks, Pascal -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] obgrep - aromaticity / kekule + molecule name bug
On Thu, Aug 8, 2013 at 12:38 AM, Pascal Muller pascal.jm.mul...@gmail.comwrote: Hi all, With file.smi being C1=CC=CC=C1 single-double c1c1 aro c1c1N obgrep C1=CC=CC=C1 file.smi gives no output. But in my opinion, all 3 molecules should be matched. No, the query string is a SMARTS, not a SMILES, so none of the molecules should match. Kekule configurations are not converted to aromatic for a SMARTS string. SMARTS are not molecules, they are pattern-matching expressions, and the electronic configuration can't be determined. If you want to search for an aromatic ring, you have to write the atoms and bonds in their aromatic form. Just to illustrate ... imagine you had a molecule that was C1=CC=CC=[C+]1=O or something else weird. It's not aromatic, but the original SMARTS *should* match it. Craig I'm pretty sure this problem was already discussed, but I found only this post http://forums.openbabel.org/Fw-Re-substructure-search-problem-td4655860.html These problems may be related? And the output of obgrep c1c1 file.smi is: c1c1single-double c1c1aro c1c1Naro It's fine, apart the 3rd compound name (there should be no compound name). In my tests, a no-name compound has the name of the preceding molecule (this preceding molecule being matched or not). Regards, Pascal -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Get 100% visibility into Java/.NET code with AppDynamics Lite! It's a free troubleshooting tool designed for production. Get down to code-level detail for bottlenecks, with 2% overhead. Download for free and get started troubleshooting in minutes. http://pubads.g.doubleclick.net/gampad/clk?id=48897031iu=/4140/ostg.clktrk___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
